Last updated: 2019-06-22

Checks: 2 0

Knit directory: BUS_notebooks_R/

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File Version Author Date Message
Rmd b208bf2 Lambda Moses 2019-06-22 Added images to index page
html cfd1e88 Lambda Moses 2019-06-22 Build site.
Rmd cdf4749 Lambda Moses 2019-06-22 Added link to kallisto bus paper
html 602b4f6 Lambda Moses 2019-06-22 Build site.
Rmd 5fe6abd Lambda Moses 2019-06-22 Updated index page for new notebooks
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Rmd 8d9fe9a Lambda Moses 2019-02-14 More detailed explanations for kallisto bus workshop
html b7b21a0 Lambda Moses 2019-02-02 Build site.
Rmd c7ecb56 Lambda Moses 2019-02-02 Added BUSpaRse installation link and note
html 85a5770 Lambda Moses 2018-12-14 Build site.
Rmd ca1d6ce Lambda Moses 2018-12-14 Clean up
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Rmd 03c3319 Lambda Moses 2018-12-14 Changed site name
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Rmd b67fc92 Lambda Moses 2018-12-14 Added 10xv3 notebook and further elaboration to 10xv2 notebook
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Rmd d5d64e9 Lambda Moses 2018-12-14 Added installation instruction
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Rmd 0dc76a9 Lambda Moses 2018-12-14 Changed to new url
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Rmd e40da79 Lambda Moses 2018-12-14 Changed URL as this repo is transferred to BUStools
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Rmd 695e202 Lambda Moses 2018-12-14 Changed name to BUSpaRse
html 9209390 Lambda Moses 2018-12-14 Update website
Rmd 37238e5 Lambda Moses 2018-12-14 Link to this GitHub repo on the website
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Rmd 1fc3e91 Lambda Moses 2018-12-14 Publish 10xv2 notebook
Rmd 55164fb Lambda Moses 2018-12-14 Start workflowr project.

bustools R notebooks

This repository has example notebooks that demonstrate usage of kallisto bus to generate gene count or (transcript compatibility count) TCC matrices from FASTQ files and some basic downstream analyses. To run the notebooks, please install kallisto, bustools, and the BUSpaRse R package.


1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (10x v2 chemistry); demonstration of bustools

1k PBMCs from a Healthy Donor (10x v3 chemistry); demonstration of TENxBUSData and BUSpaRse

RNA velocity with 10k E18 mouse neurons from 10x (coming soon)

Differential expression with equivalence classes in TCC matrix (coming soon)